Extended Data Fig. 3. Overall structure comparison and local map quality.

a. Left: Overlay of models derived from AlphaFold-Multimer prediction (white) and the cryo-EM model (color). Middle: Overlay of AlphaFold-Multimer models colored using predicted local difference distance test (pLDDT) scores for local structure accuracy. Right: Predicted aligned error (PAE) scores for distance error of the top-ranked AlphaFold-Multimer model. b. Overlay of the cryo-EM models between the Retriever-SNX17 complex (dark color, PDB 9AU7) and the Retriever apo form (light color, PDB 8SYO). c-d. Semi-transparent composite map overlayed with final model (left) (EMD-43872, PDB 9AU7) and the map colored by local resolution (right) showing the quality of the map and modeling of the SNX17 binding pocket in (c) and the SNX17 CT peptide in (d).